# HG changeset patch
# User iuc
# Date 1489273559 18000
# Node ID 993ed534cc388edee5f9203f630750d556d34317
# Parent  cde34352778e1e7eeec7f9ba249e630ad7fdab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7

diff -r cde34352778e -r 993ed534cc38 README.md
--- a/README.md	Tue Jan 31 12:46:58 2017 -0500
+++ b/README.md	Sat Mar 11 18:05:59 2017 -0500
@@ -3,7 +3,7 @@
 Copied from branch bcftools1.2:
 
 This aims to be a "faithful" rendering of the bcftool suite. I.e. options are
-presented essentially as closely to the command line version as is useful. 
+presented essentially as closely to the command line version as is useful.
 
 This may not appeal to all, if you'd like to see smaller and more dedicated
 tools (e.g. "intersect", "union" and "complement" being separate tools instead
@@ -11,12 +11,12 @@
 
 Updated for bcftools v1.3
 
-This was extended from the bcftools1.2 branch then greatly hand edited to 
+This was extended from the bcftools1.2 branch then greatly hand edited to
 group params and manage param innteractions.
 
-In the macros.xml there are macros and tokens to handle file input and output.  
+In the macros.xml there are macros and tokens to handle file input and output.
 These use the datatypes currently available in galaxy: Vcf and Bcf
-The macros take care of bgzip and indexing of inputs.  
+The macros take care of bgzip and indexing of inputs.
 
 The convert command was split into 2 tools, "convert to vcf" and "convert from vcf"
 
@@ -27,7 +27,7 @@
 - cnv needs an input.vcf for testing, runs with bcftools cnv -s "HG00101" -o 'HG00101/' -p 5 mpileup.vcf
 - roh needs a more useful input.vcf for testing
 - plugin color chrs
-- plugin frameshifts 
+- plugin frameshifts
 
 ## Status
 
diff -r cde34352778e -r 993ed534cc38 bcftools_view.xml
--- a/bcftools_view.xml	Tue Jan 31 12:46:58 2017 -0500
+++ b/bcftools_view.xml	Sat Mar 11 18:05:59 2017 -0500
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">
     <description>VCF/BCF conversion, view, subset and filter VCF/BCF files</description>
     <macros>
         <token name="@EXECUTABLE@">view</token>
@@ -31,36 +31,36 @@
 
 ## Filter section
 #set $section = $sec_filter
-#if $section.min_ac:
-  --min-ac "${section.min_ac}"
+#if str($section.min_ac)
+  --min-ac ${section.min_ac}
 #end if
-#if $section.max_ac:
-  --max-ac "${section.max_ac}"
+#if str($section.max_ac)
+  --max-ac ${section.max_ac}
 #end if
 #if str($section.select_genotype) != "__none__":
   --genotype "${section.select_genotype}"
 #end if
 ## known or novel
 #if $section.known_or_novel:
-${section.known_or_novel}
+  ${section.known_or_novel}
 #end if
-#if $section.min_alleles:
-  --min-alleles "${section.min_alleles}"
+#if str($section.min_alleles)
+  --min-alleles ${section.min_alleles}
 #end if
-#if $section.max_alleles:
-  --max-alleles "${section.max_alleles}"
+#if str($section.max_alleles)
+  --max-alleles ${section.max_alleles}
 #end if
 #if $section.phased:
-${section.phased}
+  ${section.phased}
 #end if
-#if $section.min_af:
-  --min-af "${section.min_af}"
+#if str($section.min_af)
+  --min-af ${section.min_af}
 #end if
-#if $section.max_af:
-  --max-af "${section.max_af}"
+#if str($section.max_af)
+  --max-af ${section.max_af}
 #end if
 #if $section.uncalled:
-${section.uncalled}
+  ${section.uncalled}
 #end if
 #if $section.types:
   --types "${section.types}"
@@ -69,17 +69,17 @@
   --exclude-types "${section.exclude_types}"
 #end if
 #if $section.private:
-${section.private}
+  ${section.private}
 #end if
 
 ## Output section
 #set $section = $sec_output
 ${section.drop_genotypes}
 #if $section.header:
-${section.header}
+  ${section.header}
 #end if
-#if $section.compression_level:
-  --compression-level "${section.compression_level}"
+#if str($section.compression_level)
+  --compression-level ${section.compression_level}
 #end if
 
 #set $section = $sec_restrict
@@ -94,7 +94,7 @@
 
 ## Primary Input/Outputs
 @INPUT_FILE@
-> "$output_file"
+> '$output_file'
 ]]>
     </command>
     <inputs>
@@ -108,17 +108,17 @@
         </section>
         <section name="sec_subset" expanded="false" title="Subset Options">
             <expand macro="macro_samples" />
-            <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples" 
+            <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples"
                    help="Only warn about unknown subset samples" />
-            <param name="no_update" type="boolean" truevalue="--no-update" falsevalue="" label="No Update" 
+            <param name="no_update" type="boolean" truevalue="--no-update" falsevalue="" label="No Update"
                    help="Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)" />
-            <param name="trim_alt_alleles" type="boolean" truevalue="--trim-alt-alleles" falsevalue="" label="Trim Alt Alleles" 
+            <param name="trim_alt_alleles" type="boolean" truevalue="--trim-alt-alleles" falsevalue="" label="Trim Alt Alleles"
                    help="Trim alternate alleles not seen in the subset" />
         </section>
         <section name="sec_filter" expanded="false" title="Filter Options">
-            <param name="min_ac" type="integer" label="Min Ac" optional="True" 
+            <param name="min_ac" type="integer" label="Min Ac" optional="True"
                    help="(-c --min-ac) Minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
-            <param name="max_ac" type="integer" label="Max Ac" optional="True" 
+            <param name="max_ac" type="integer" label="Max Ac" optional="True"
                    help="(-C --max-ac) Maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
             <param name="select_genotype" type="select">
                 <option value="__none__" selected="True">No selection</option>
@@ -129,7 +129,7 @@
 
             <param name="types" type="select" label="Select Types"  multiple="true" optional="True">
                 <help>
-                 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested. 
+                 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested.
                  Types are determined by comparing the REF and ALT alleles in the VCF record.
                 </help>
                 <expand macro="macro_types_options" />
@@ -137,7 +137,7 @@
 
             <param name="exclude_types" type="select" label="Exclude Types"  multiple="true" optional="True">
                 <help>
-                 List of variant types to exclude. Site is excluded if any of the ALT alleles is of the type requested. 
+                 List of variant types to exclude. Site is excluded if any of the ALT alleles is of the type requested.
                  Types are determined by comparing the REF and ALT alleles in the VCF record.
                 </help>
                 <expand macro="macro_types_options" />
@@ -149,23 +149,23 @@
                   <option value="--known">(-n) print known sites only (ID column is not ".")</option>
               </param>
 
-              <param name="min_alleles" type="integer" label="Min Alleles" optional="True" 
+              <param name="min_alleles" type="integer" label="Min Alleles" optional="True"
                      help="(-m) Minimum number of alleles listed in REF and ALT (e.g. -m2)" />
-              <param name="max_alleles" type="integer" label="Max Alleles" optional="True" 
+              <param name="max_alleles" type="integer" label="Max Alleles" optional="True"
                      help="(-M) Maximum number of alleles listed in REF and ALT (e.g. -M2 for biallelic sites)" />
 
               <param name="phased" type="select" label="filter phased" optional="true">
                   <help>
-                  Haploid genotypes are considered phased. Missing genotypes considered unphased unless the phased bit is set. 
+                  Haploid genotypes are considered phased. Missing genotypes considered unphased unless the phased bit is set.
                   </help>
                   <option value="--phased">(-p) print sites where all samples are phased</option>
                   <option value="--exclude-phased">(-P) exclude sites where all samples are phased</option>
               </param>
 
               <!-- TODO optional select for type: nref,alt1,minor,major,sum -->
-              <param name="min_af" type="float" label="Min Af" optional="True" 
+              <param name="min_af" type="float" label="Min Af" optional="True"
                      help="(-q) Minimum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
-              <param name="max_af" type="float" label="Max Af" optional="True" 
+              <param name="max_af" type="float" label="Max Af" optional="True"
                      help="(-Q) Maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
 
               <param name="uncalled" type="select" label="filter on genotype uncalled" optional="true">
@@ -185,15 +185,15 @@
         </section>
 
         <section name="sec_output" expanded="false" title="Output Options">
-            <param name="drop_genotypes" type="boolean" truevalue="--drop-genotypes" falsevalue="" label="Drop Genotypes" 
+            <param name="drop_genotypes" type="boolean" truevalue="--drop-genotypes" falsevalue="" label="Drop Genotypes"
                    help="Drop individual genotype information (after subsetting if -s option set)" />
             <param name="header" type="select" label="output header" optional="true">
                 <option value="--no-header">(-h) no-header</option>
                 <option value="--header-only">(-H) header-only</option>
             </param>
-            <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True" 
+            <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True"
                    help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" />
-            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File" 
+            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File"
                    help="Inverts the query/filtering applied by Targets File" />
         </section>
         <expand macro="macro_select_output_type" />
@@ -211,8 +211,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="rs2298108" /> 
-                    <not_has_text text="rs6111385" /> 
+                    <has_text text="rs2298108" />
+                    <not_has_text text="rs6111385" />
                 </assert_contents>
             </output>
         </test>
@@ -225,8 +225,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="8657215" /> 
-                    <not_has_text text="rs6111385" /> 
+                    <has_text text="8657215" />
+                    <not_has_text text="rs6111385" />
                 </assert_contents>
             </output>
         </test>
@@ -240,8 +240,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="rs6111385" /> 
-                    <not_has_text text="8657215" /> 
+                    <has_text text="rs6111385" />
+                    <not_has_text text="8657215" />
                 </assert_contents>
             </output>
         </test>
@@ -252,8 +252,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="rs62584840" /> 
-                    <not_has_text text="8657215" /> 
+                    <has_text text="rs62584840" />
+                    <not_has_text text="8657215" />
                 </assert_contents>
             </output>
         </test>
@@ -263,8 +263,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="rs5939407" /> 
-                    <not_has_text text="8657215" /> 
+                    <has_text text="rs5939407" />
+                    <not_has_text text="8657215" />
                 </assert_contents>
             </output>
         </test>
@@ -274,8 +274,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="rs78249411" /> 
-                    <not_has_text text="rs6111385" /> 
+                    <has_text text="rs78249411" />
+                    <not_has_text text="rs6111385" />
                 </assert_contents>
             </output>
         </test>
@@ -285,8 +285,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="rs6111385" /> 
-                    <not_has_text text="rs78249411" /> 
+                    <has_text text="rs6111385" />
+                    <not_has_text text="rs78249411" />
                 </assert_contents>
             </output>
         </test>
@@ -300,8 +300,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="##bcftools_viewCommand" /> 
-                    <not_has_text text="rs78249411" /> 
+                    <has_text text="##bcftools_viewCommand" />
+                    <not_has_text text="rs78249411" />
                 </assert_contents>
             </output>
         </test>
@@ -312,8 +312,8 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <not_has_text text="##bcftools_viewCommand" /> 
-                    <has_text text="5464562" /> 
+                    <not_has_text text="##bcftools_viewCommand" />
+                    <has_text text="5464562" />
                 </assert_contents>
             </output>
         </test>
@@ -324,9 +324,9 @@
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <not_has_text text="##FORMAT=&lt;ID=GT" /> 
-                    <not_has_text text="rs62584840" /> 
-                    <has_text text="2343543" /> 
+                    <not_has_text text="##FORMAT=&lt;ID=GT" />
+                    <not_has_text text="rs62584840" />
+                    <has_text text="2343543" />
                 </assert_contents>
             </output>
         </test>
diff -r cde34352778e -r 993ed534cc38 macros.xml
--- a/macros.xml	Tue Jan 31 12:46:58 2017 -0500
+++ b/macros.xml	Sat Mar 11 18:05:59 2017 -0500
@@ -1,6 +1,5 @@
-
 <macros>
-  <token name="@VERSION@">1.3</token>
+  <token name="@VERSION@">1.3.1</token>
   <xml name="stdio">
     <stdio>
       <exit_code range="1:" />
@@ -11,13 +10,10 @@
   </xml>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.3">bcftools</requirement>
+      <requirement type="package" version="1.3.1">bcftools</requirement>
       <!-- conda dependency -->
-      <requirement type="package" version="1.3">htslib</requirement>
-      <!-- htslib provides tabix and bgzip
-      <requirement type="package" version="0.2.6">tabix</requirement>
-      -->
-      <requirement type="package" version="1.2">samtools</requirement>
+      <requirement type="package" version="1.3.2">htslib</requirement>
+      <yield />
     </requirements>
   </xml>
   <xml name="version_command">
@@ -48,20 +44,20 @@
 ## May need to symlink input if there is an associated
 #set $input_vcf = 'input.vcf.gz'
 #if $input_file.is_of_type('vcf')
-  bgzip -c "$input_file" > $input_vcf &&
+  bgzip -c '$input_file' > $input_vcf &&
   bcftools index $input_vcf &&
 #elif $input_file.is_of_type('vcf_bgzip')
-  ln -s "$input_file" $input_vcf
+  ln -s '$input_file' $input_vcf
 #elif $input_file.is_of_type('bcf')
   #set $input_vcf = 'input.bcf'
-  ln -s "$input_file" $input_vcf &&
+  ln -s '$input_file' $input_vcf &&
   #if $input_file.metadata.bcf_index:
-    ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
+    ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
   #else
     bcftools index $input_vcf &&
   #end if
 #elif $input_file.is_of_type('bcf_bgzip')
-  ln -s "$input_file" $input_vcf
+  ln -s '$input_file' $input_vcf
 #end if
 ]]>
   </token>
@@ -77,24 +73,23 @@
 ## May need to symlink input if there is an associated
 #set $input_vcfs = []
 #set $vcfs_list_file = 'vcfs_list'
-#for (i,input_file) in enumerate($input_files):
+#for (i, input_file) in enumerate($input_files):
   #set $input_vcf = 'input' + str($i) + '.vcf.gz'
   #if $input_file.is_of_type('vcf')
-    bgzip -c "$input_file" > $input_vcf &&
+    bgzip -c '$input_file' > $input_vcf &&
     bcftools index $input_vcf &&
   #elif $input_file.is_of_type('vcf_bgz')
-    ln -s "$input_file" $input_vcf
+    ln -s '$input_file' $input_vcf
   #elif $input_file.is_of_type('bcf')
     #set $input_vcf = 'input' + str($i) + '.bcf.gz'
-    ## bgzip -c "$input_file" > $input_vcf &&
-    ln -s "$input_file" $input_vcf &&
+    ln -s '$input_file' $input_vcf &&
     #if $input_file.metadata.bcf_index:
-      ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
+      ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
     #else
       bcftools index $input_vcf &&
     #end if
   #elif $input_file.is_of_type('bcfvcf_bgz')
-    ln -s "$input_file" $input_vcf &&
+    ln -s '$input_file' $input_vcf &&
   #end if
   echo '$input_vcf' >> $vcfs_list_file &&
   $input_vcfs.append($input_vcf)
@@ -109,23 +104,23 @@
   </token>
 
   <xml name="macro_fasta_ref">
-    <param name="fasta_ref" type="data" format="data" label="Fasta Ref" optional="True" help="reference sequence in fasta format" />
+    <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" label="Reference sequence in FASTA format" optional="True" />
   </xml>
   <token name="@PREPARE_FASTA_REF@">
 <![CDATA[
 #set $input_fa_ref = None
 #if 'fasta_ref' in $section and $section.fasta_ref:
   #set $input_fa_ref = 'ref.fa'
-  ln -s $section.fasta_ref $input_fa_ref &&
+  ln -s '$section.fasta_ref' $input_fa_ref &&
   samtools faidx $input_fa_ref &&
 #end if
 ]]>
   </token>
   <token name="@FASTA_REF@">
 #if $input_fa_ref is not None:
-  --fasta-ref  "$input_fa_ref"
+  --fasta-ref $input_fa_ref
 #elif 'fasta_ref' in $section and $section.fasta_ref:
-  --fasta-ref "${section.fasta_ref}"
+  --fasta-ref '${section.fasta_ref}'
 #end if
   </token>
 
@@ -151,24 +146,24 @@
 
 
   <xml name="macro_AF_file">
-    <param name="AF_file" type="data" format="data" label="Af File" optional="True" help="read allele frequencies from file (CHR\tPOS\tREF,ALT\tAF)" />
+    <param name="AF_file" argument="--AF-file" type="data" format="tabular" label="Allele frequencies file" optional="True" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
   </xml>
   <!-- This may need to bgzip and tabix the file -->
   <token name="@PREPARE_AF_FILE@">
 <![CDATA[
 #if 'AF_file' in $section and $section.AF_file:
-#pass
+    #pass
 #end if
 ]]>
   </token>
   <token name="@AF_FILE@">
 #if 'AF_file' in $section and $section.AF_file:
-  --AF-file "${section.AF_file}"
+  --AF-file '${section.AF_file}'
 #end if
   </token>
 
   <xml name="macro_estimate_AF">
-      <param name="estimate_AF" type="data" format="data" label="Estimate Af" optional="True" help="calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
+      <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" label="Estimate allele frequency" optional="True" help="calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
   </xml>
   <token name="@ESTIMATE_AF@">
 #if 'estimate_AF' in $section and $section.estimate_AF:
@@ -222,7 +217,7 @@
   </xml>
   <token name="@COLLAPSE@">
 #if $section.collapse:
-  --collapse "${section.collapse}"
+  --collapse ${section.collapse}
 #end if
   </token>
 
@@ -234,7 +229,7 @@
   </xml>
   <token name="@APPLY_FILTERS@">
 #if $section.apply_filters:
-  --apply-filters "${section.apply_filters}"
+  --apply-filters '${section.apply_filters}'
 #end if
   </token>
 
@@ -286,9 +281,9 @@
   </xml>
   <token name="@REGIONS@">
 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
-  --regions "$section.regions.regions"
+  --regions '$section.regions.regions'
 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
-  --regions-file "$section.regions.regions_file"
+  --regions-file '$section.regions.regions_file'
 #end if
   </token>
 
@@ -351,7 +346,7 @@
   --targets-file "${section.targets.invert_targets_file}${targets_path}"
 #else:
   #if $section.targets.targets_src == 'targets' and $section.targets.targets != '':
-    --targets "${section.targets.invert_targets_file}${section.targets.targets}"
+    --targets '${section.targets.invert_targets_file}${section.targets.targets}'
   #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
     --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
   #end if
@@ -375,7 +370,7 @@
 #set $samples_defined = False
 #if str($section.samples) != '':
   #set $samples_defined = True
-  --samples "${section.invert_samples}${section.samples}"
+  --samples '${section.invert_samples}${section.samples}'
 #end if
 #if $section.samples_file:
   #set $samples_defined = True
@@ -388,7 +383,7 @@
   </xml>
   <token name="@SAMPLE@">
 #if $section.sample:
-  --sample "${section.sample}"
+  --sample '${section.sample}'
 #end if
   </token>
 
@@ -425,7 +420,7 @@
   </xml>
   <token name="@COLUMNS@">
 #if $section.columns != '':
-  --columns "${section.columns}"
+  --columns '${section.columns}'
 #end if
   </token>
 
@@ -453,8 +448,7 @@
 This Galaxy tool recommends using the compressed BCF format
 as piping is not implemented, and uncompressed data would
 use unnecessary amounts of space.
-
-]]></token>
+  ]]></token>
   <token name="@REGIONS_HELP@">
       <![CDATA[
 Region Selections
@@ -475,8 +469,7 @@
 FILE. Note that overlapping regions in FILE can result in
 duplicated out of order positions in the output. This option
 requires indexed VCF/BCF files.
-
-]]></token>
+  ]]></token>
   <token name="@TARGETS_HELP@"><![CDATA[
 Targets
 -------
@@ -541,7 +534,6 @@
 | id         | only records with identical ID column are compatible.          |
 |            | Supportedby bcftools merge only.                               |
 +------------+----------------------------------------------------------------+
-
   </token>
 
   <token name="@EXPRESSIONS_HELP@">
@@ -666,10 +658,5 @@
       ID=@file       .. selects lines with ID present in the file
       ID!=@~/file    .. skip lines with ID present in the ~/file
       MAF[0]<0.05    .. select rare variants at 5% cutoff
-
-]]></token>
-
-
-
-
+  ]]></token>
 </macros>
diff -r cde34352778e -r 993ed534cc38 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jan 31 12:46:58 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="bcftools" version="1.3">
-        <repository changeset_revision="43a9aebf3adb" name="package_bcftools_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="tabix" version="0.2.6">
-        <repository changeset_revision="389d2376b60b" name="package_tabix_0_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="samtools" version="1.2">
-        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>